1TZD - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE

Authors :   G. J. Miller, J. H. Hurley

Date :   09 Jul 04 (Deposition) - 21 Sep 04 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Inositol Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. J. Miller, J. H. Hurley
Crystal Structure Of The Catalytic Core Of Inositol 1, 4, 5-Trisphosphate 3-Kinase
Mol. Cell V. 15 703 2004
PubMed-ID: 15350215 | Reference-DOI: 10.1016/J.MOLCEL.2004.08.005

Molecule 1 - INOSITOL-TRISPHOSPHATE 3-KINASE A
	Chains	:	A, B
	EC Number	:	2.7.1.127
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST15
	Expression System Strain	:	BL(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC CORE
	Gene	:	ITPKA
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	INOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE A, IP3K A, IP3 3- KINASE A

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 17)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ADP B:1 , ASP B:414 , HOH B:472 , HOH B:634	BINDING SITE FOR RESIDUE MG A 2
2	AC2	SOFTWARE	LYS A:207 , GLN A:247 , ASP A:248 , LEU A:249 , ASP A:260 , ASP A:414 , HOH A:500 , HOH A:511 , HOH A:513 , HOH A:529 , HOH A:574 , HOH A:612	BINDING SITE FOR RESIDUE ADP A 1
3	AC3	SOFTWARE	MG A:2 , ILE B:205 , LYS B:207 , GLN B:247 , LEU B:249 , ASP B:260 , LEU B:399 , ILE B:413 , ASP B:414 , HOH B:508 , HOH B:634 , HOH B:644	BINDING SITE FOR RESIDUE ADP B 1

(no "SS Bond" information available for 1TZD)

(no "Cis Peptide Bond" information available for 1TZD)

(no "SAP(SNP)/Variant" information available for 1TZD)

(no "PROSITE Motif" information available for 1TZD)

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000007247	1	ENSRNOE00000050005	chr3:106257482-106258009	528	IP3KA_RAT	1-161	161	0	-	-
1.2	ENSRNOT00000007247	2	ENSRNOE00000050238	chr3:106264112-106264208	97	IP3KA_RAT	162-194	33	0	-	-
1.3	ENSRNOT00000007247	3	ENSRNOE00000050424	chr3:106264284-106264500	217	IP3KA_RAT	194-266	73	2	A:203-266 (gaps) B:203-266 (gaps)	64 64
1.4	ENSRNOT00000007247	4	ENSRNOE00000050612	chr3:106264597-106264801	205	IP3KA_RAT	266-334	69	2	A:266-334 (gaps) B:266-334 (gaps)	69 69
1.5	ENSRNOT00000007247	5	ENSRNOE00000050796	chr3:106265018-106265119	102	IP3KA_RAT	335-368	34	2	A:335-368 B:335-368	34 34
1.6	ENSRNOT00000007247	6	ENSRNOE00000050978	chr3:106265396-106265467	72	IP3KA_RAT	369-392	24	2	A:369-392 B:369-392	24 24
1.7	ENSRNOT00000007247	7	ENSRNOE00000051155	chr3:106265579-106266160	582	IP3KA_RAT	393-459	67	2	A:393-458 B:393-457	66 65

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:243
 aligned with IP3KA_RAT | P17105 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:256
                                   212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452      
            IP3KA_RAT   203 GLILKRSSEPEHYCLVRLMADVLRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVTRVFEEFMQGDAEVLKRYLNRLQQIRDTLEISDFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILANLAE 458
               SCOP domains d1tzda_ A: Inositol 1,4,5-trisphos       phate 3-kinase A, IP3K A                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhhhhhhhhhhhhhhh.......-------.eee.........eeeee.......hhhhhhhhhhh.....hhhhhh.......hhhhhhh------hhhhhhhhhhh........eeeee.....ee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhh......eeeeee.....eeeeee...........................hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:203-266 (gaps) UniProt: 194-266 [INCOMPLETE]   --------------------------------------------------------------------Exon 1.5  PDB: A:335-368          Exon 1.6  PDB: A:369-392Exon 1.7  PDB: A:393-458 UniProt: 393-459 [INCOMPLETE]             Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.4  PDB: A:266-334 (gaps) UniProt: 266-334                     ---------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1tzd A 203 GLILKRSSEPEHYCmVRLmADVLRGCVPAFHGVV-------LQLQDLLDGFDGPCVLDCKmGVRTYLEEELTKARERPKLRKDmYKKmLAVDPEAPTEEEHA------PRYmQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVTRVFEEFmQGDAEVLKRYLNRLQQIRDTLEISDFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPNGQILDHRRPWEEGNREDGYLLGLDNLIGILANLAE 458
                                   212    |  222       232   |     - |     252       262|      272       282   |   292       302 |     312 |     322       332       342       352       362       372       382       392       402       412       422       432       442       452      
                                        217-MSE            236     244                263-MSE                286-MSE           304    311  |                                            361-MSE                                                                                             
                                            221-MSE                                                              290-MSE                 314-MSE

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with IP3KA_RAT | P17105 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:255
                                   212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452     
            IP3KA_RAT   203 GLILKRSSEPEHYCLVRLMADVLRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVTRVFEEFMQGDAEVLKRYLNRLQQIRDTLEISDFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILANLA 457
               SCOP domains d1tzdb_ B: Inositol 1,4,5-trisphos       phate 3-kinase A, IP3K A                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------       IPK-1tzdB01 B:244-454                                                                                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) ----------------------------------       IPK-1tzdB02 B:244-454                                                                                                                                                                                              --- Pfam domains (2)
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhh.......-------.............eeeeeee.....hhhhhhh.......hhhhhhhhhh............------hhhhhhhhhh.......eeeeeee.....ee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....eee...eeeeee.....eeeeee....eee....................hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:203-266 (gaps) UniProt: 194-266 [INCOMPLETE]   --------------------------------------------------------------------Exon 1.5  PDB: B:335-368          Exon 1.6  PDB: B:369-392Exon 1.7  PDB: B:393-457 UniProt: 393-459 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.4  PDB: B:266-334 (gaps) UniProt: 266-334                     --------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1tzd B 203 GLILKRSSEPEHYCmVRLmADVLRGCVPAFHGVV-------LQLQDLLDGFDGPCVLDCKmGVRTYLEEELTKARERPKLRKDmYKKmLAVDPEAPTEEEHA------PRYmQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVTRVFEEFmQGDAEVLKRYLNRLQQIRDTLEISDFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPNGQILDHRRPWEEGNREDGYLLGLDNLIGILANLA 457
                                   212    |  222       232   |     - |     252       262|      272       282   |   292       302 |     312 |     322       332       342       352       362       372       382       392       402       412       422       432       442       452     
                                        217-MSE            236     244                263-MSE                286-MSE           304    311  |                                            361-MSE                                                                                            
                                            221-MSE                                                              290-MSE                 314-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: SAICAR synthase-like (28)

Superfamily: SAICAR synthase-like (28)

Family: Inositol polyphosphate kinase (IPK) (6)

Protein domain: Inositol 1,4,5-trisphosphate 3-kinase A, IP3K A (4)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

1a	d1tzda_	A:
1b	d1tzdb_	B:

(no "CATH Domain" information available for 1TZD)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: IPK] (3)

Family: IPK (3)

Rattus norvegicus (Rat) (1)

1a	IPK-1tzdB01	B:244-454
1b	IPK-1tzdB02	B:244-454

Asymmetric Unit(hide GO term definitions)

Chain A,B (IP3KA_RAT | P17105)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0048365	Rac GTPase binding	Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0004683	calmodulin-dependent protein kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
	GO:0008440	inositol-1,4,5-trisphosphate 3-kinase activity	Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0097062	dendritic spine maintenance	The organization process that preserves a dendritic spine in a stable functional or structural state. A dendritic spine is a specialized protrusion from a neuronal dendrite and is involved in synaptic transmission.
	GO:0006020	inositol metabolic process	The chemical reactions and pathways involving inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	GO:0061003	positive regulation of dendritic spine morphogenesis	Any process that increases the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0048167	regulation of synaptic plasticity	A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
cellular component
	GO:0043197	dendritic spine	A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.

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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 17)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (5, 10)

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